3LMY | pdb_00003lmy

The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3lmyb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3lmyb1	Alpha and beta proteins (a+b)	Zincin-like	beta-N-acetylhexosaminidase-like domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3lmya2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3lmya1	Alpha and beta proteins (a+b)	Zincin-like	beta-N-acetylhexosaminidase-like domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	beta-N-acetylhexosaminidase-like domain	8037319	3000192	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8037318	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-N-acetylhexosaminidase-like domain	8037319	3000192	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8037318	3000313	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e3lmyB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: AAA	F:	ECOD (20:10:01)
A		e3lmyA1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: Rieske	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.379.10	Alpha Beta	2-Layer Sandwich	Chitobiase	domain 2	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	3.30.379.10	Alpha Beta	2-Layer Sandwich	Chitobiase	domain 2	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14845	beta-acetyl hexosaminidase like (Glycohydro_20b2)	beta-acetyl hexosaminidase like		Domain
A, B	PF00728	Glycosyl hydrolase family 20, catalytic domain (Glyco_hydro_20)	Glycosyl hydrolase family 20, catalytic domain	This domain has a TIM barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Beta-hexosaminidase subunit beta	hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity binding carbohydrate binding protein-containing complex binding UDP-glycosyltransferase activity glycosyltransferase activity acetylglucosaminyltransferase activity transferase activity hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity binding carbohydrate binding protein-containing complex binding UDP-glycosyltransferase activity glycosyltransferase activity acetylglucosaminyltransferase activity transferase activity hexosyltransferase activity identical protein binding protein binding	carbohydrate derivative catabolic process dermatan sulfate proteoglycan metabolic process glycoprotein catabolic process catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process dermatan sulfate proteoglycan catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process carbohydrate derivative catabolic process dermatan sulfate proteoglycan metabolic process glycoprotein catabolic process catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process dermatan sulfate proteoglycan catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process proteoglycan catabolic process proteoglycan metabolic process behavior multicellular organismal process locomotory behavior chondroitin sulfate proteoglycan metabolic process chondroitin sulfate proteoglycan catabolic process developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation cell differentiation anatomical structure development germ cell development glial cell migration nervous system development neurogenesis multicellular organism development gliogenesis astrocyte cell migration cell migration cell motility system development skeletal system development carbohydrate derivative biosynthetic process glycoprotein biosynthetic process N-glycan processing macromolecule biosynthetic process protein N-linked glycosylation biosynthetic process sphingolipid catabolic process ceramide metabolic process ganglioside catabolic process glycosphingolipid catabolic process lipid catabolic process glycolipid metabolic process glycosphingolipid metabolic process liposaccharide metabolic process sphingolipid metabolic process glycolipid catabolic process ceramide catabolic process ganglioside metabolic process lipid metabolic process fertilization single fertilization inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis system process nervous system process neuromuscular process neuromuscular process controlling balance lipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process amino sugar metabolic process N-acetylglucosamine metabolic process cellular component organization lysosome organization organelle organization vacuole organization lytic vacuole organization cellular component organization or biogenesis multi-multicellular organism process penetration of zona pellucida regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis sensory perception sensory perception of sound sensory perception of mechanical stimulus carbohydrate metabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process lipid storage nutrient storage myelination axon ensheathment ensheathment of neurons glycosaminoglycan metabolic process aminoglycan metabolic process male mating behavior male courtship behavior reproductive behavior courtship behavior mating behavior regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process hyaluronan catabolic process aminoglycan catabolic process glycosaminoglycan catabolic process hyaluronan metabolic process neuron cellular homeostasis	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular vesicle endomembrane system cytoplasmic vesicle secretory granule secretory vesicle cortical granule cytoplasmic vesicle lumen vesicle lumen azurophil granule secretory granule lumen azurophil granule lumen primary lysosome beta-N-acetylhexosaminidase complex protein-containing complex catalytic complex acrosomal vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029019	Beta-hexosaminidase, eukaryotic type, N-terminal	Domain
A, B	IPR015883	Beta-hexosaminidase, catalytic domain	Domain
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR029018	Beta-hexosaminidase-like, domain 2	Homologous Superfamily
A, B	IPR025705	Beta-hexosaminidase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P07686	Sandhoff disease gangliosidosis GM2 gangliosidosis Juvenile Sandhoff Disease lung cancer neurodegenerative disease acute kidney failure acute myeloid leukemia breast cancer Duchenne muscular dystrophy IgA glomerulonephritis intellectual disability lymphoplasmacytic lymphoma ovarian cancer sphingolipidosis Sandhoff disease gangliosidosis GM2 gangliosidosis Juvenile Sandhoff Disease lung cancer neurodegenerative disease acute kidney failure acute myeloid leukemia breast cancer Duchenne muscular dystrophy IgA glomerulonephritis intellectual disability lymphoplasmacytic lymphoma ovarian cancer sphingolipidosis dermatomyositis glioblastoma inborn errors of metabolism juvenile dermatomyositis large cell medulloblastoma lysosomal storage disease plasma cell myeloma diabetes mellitus esophageal adenocarcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.